Batch Processing

  1. Repeat the exercise from the Batch Processing Lecture (7th April), but do it using real data sets rather than purely simulated. Check with folks in your lab to see if there are multiple data sets available for analysis. Stick to simple data analyses and graphics, but try to set it up as a batch process that will work on multiple files and save summary results to a common file. If you can only find a data set, then simulate a couple of others by following the methods in Homework #6 by selecting appropriate statistical distributions and estimating parameters for those from the real data.

Hopefully, this exercise will contribute to some actual work that you are trying to do in your research!

# Batch processing to create graphs for SelectPos

# load data ----------------------------------
library(ggplot2)
library(data.table)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:data.table':
## 
##     between, first, last
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
load("/Users/skogut/Desktop/Thesis/SelectPosVACC.rda")
SelectPos<- arrange(SelectPos, by= desc(Slope))
SelectPos$ERV<- gsub("X", "", SelectPos$ERV)
SelectPairs<- SelectPos[1:1000, 1:2]
SelectPairs$ERV<- gsub("\\.", "-", SelectPairs$ERV)
print(SelectPairs)
##          ERV         Transcript
## 1        727  ENST00000361381.2
## 2        727  ENST00000361453.3
## 3       K-32  ENST00000387347.2
## 4        727  ENST00000361567.2
## 5       2758  ENST00000361453.3
## 6        727  ENST00000361390.2
## 7       2758  ENST00000361381.2
## 8        727  ENST00000361335.1
## 9       2758  ENST00000361335.1
## 10      2758  ENST00000387347.2
## 11      4666  ENST00000387347.2
## 12      4666  ENST00000361453.3
## 13      2758  ENST00000361567.2
## 14      5110  ENST00000627981.1
## 15      2758  ENST00000361390.2
## 16       727  ENST00000361789.2
## 17      5109  ENST00000627981.1
## 18      4666  ENST00000361381.2
## 19      4666  ENST00000361335.1
## 20       727  ENST00000361624.2
## 21      2593  ENST00000627981.1
## 22      2758  ENST00000361789.2
## 23      4666  ENST00000361390.2
## 24      4666  ENST00000361567.2
## 25      5047  ENST00000627981.1
## 26      2758  ENST00000361624.2
## 27      2758  ENST00000389680.2
## 28      4851  ENST00000387347.2
## 29      4851  ENST00000361453.3
## 30      4641  ENST00000389680.2
## 31      4851  ENST00000361381.2
## 32       727  ENST00000361681.2
## 33      K-32  ENST00000361381.2
## 34      4666  ENST00000361789.2
## 35      4666  ENST00000361624.2
## 36      K-32  ENST00000389680.2
## 37      4851  ENST00000361335.1
## 38      4851  ENST00000361567.2
## 39      K-32  ENST00000361335.1
## 40      2758  ENST00000361899.2
## 41      4851  ENST00000361390.2
## 42      K-32  ENST00000361567.2
## 43       935  ENST00000387347.2
## 44      1716  ENST00000387347.2
## 45      3184  ENST00000387347.2
## 46      2758  ENST00000361681.2
## 47      4894  ENST00000387347.2
## 48      K-32  ENST00000361453.3
## 49      K-32  ENST00000361624.2
## 50      4606  ENST00000387347.2
## 51      4894  ENST00000361453.3
## 52      3184  ENST00000361453.3
## 53      4851  ENST00000361789.2
## 54      4851  ENST00000389680.2
## 55      4666  ENST00000361899.2
## 56      K-32  ENST00000361390.2
## 57      4894  ENST00000361381.2
## 58      4851  ENST00000361624.2
## 59      3184  ENST00000361381.2
## 60      2758  ENST00000361739.1
## 61      4894  ENST00000361335.1
## 62       727  ENST00000361851.1
## 63      3184  ENST00000361335.1
## 64       727  ENST00000362079.2
## 65      4666  ENST00000361681.2
## 66      K-32  ENST00000361789.2
## 67      5110  ENST00000629969.1
## 68      4894  ENST00000361567.2
## 69      1393  ENST00000387347.2
## 70      4894  ENST00000361390.2
## 71      3184  ENST00000361390.2
## 72      3375  ENST00000387347.2
## 73      2758  ENST00000361851.1
## 74      2758  ENST00000514057.1
## 75      3184  ENST00000361567.2
## 76      3375  ENST00000361381.2
## 77      3375  ENST00000361567.2
## 78      3375  ENST00000361453.3
## 79       727  ENST00000361227.2
## 80      4851  ENST00000361899.2
## 81      5109  ENST00000629969.1
## 82      4894  ENST00000389680.2
## 83      K-32  ENST00000361899.2
## 84      3184  ENST00000389680.2
## 85      3375  ENST00000361390.2
## 86      4851  ENST00000361681.2
## 87      1393  ENST00000361453.3
## 88      3184  ENST00000361789.2
## 89      4894  ENST00000361789.2
## 90      4666  ENST00000361851.1
## 91       935  ENST00000361453.3
## 92      4894  ENST00000361624.2
## 93      3184  ENST00000361624.2
## 94      2758  ENST00000362079.2
## 95      2758  ENST00000361227.2
## 96      1393  ENST00000361381.2
## 97      4666  ENST00000514057.1
## 98      K-32  ENST00000361681.2
## 99       935  ENST00000389680.2
## 100     1716  ENST00000389680.2
## 101     1716  ENST00000361567.2
## 102     4606  ENST00000361567.2
## 103     5047  ENST00000629969.1
## 104     3375  ENST00000361335.1
## 105      935  ENST00000361381.2
## 106     1393  ENST00000361567.2
## 107     1393  ENST00000361335.1
## 108      727  ENST00000457540.1
## 109     4118  ENST00000361453.3
## 110     1393  ENST00000361390.2
## 111     3375  ENST00000389680.2
## 112      935  ENST00000361335.1
## 113     1079  ENST00000387347.2
## 114     3375  ENST00000361789.2
## 115     4851  ENST00000361739.1
## 116     4118  ENST00000387347.2
## 117     4666  ENST00000362079.2
## 118     K-32  ENST00000362079.2
## 119     4118  ENST00000361381.2
## 120     1393  ENST00000389680.2
## 121     4666  ENST00000361227.2
## 122   UID-51  ENST00000387347.2
## 123     4118  ENST00000361335.1
## 124      935  ENST00000361390.2
## 125     4606  ENST00000361381.2
## 126      935  ENST00000361567.2
## 127     4894  ENST00000361899.2
## 128     4851  ENST00000361851.1
## 129     4851  ENST00000514057.1
## 130     2758  ENST00000457540.1
## 131     3184  ENST00000361899.2
## 132     K-32  ENST00000361739.1
## 133     4118  ENST00000361390.2
## 134      935  ENST00000361789.2
## 135     3375  ENST00000361624.2
## 136     4118  ENST00000361567.2
## 137     4606  ENST00000361390.2
## 138     1393  ENST00000361789.2
## 139     2593  ENST00000629969.1
## 140     3375  ENST00000361899.2
## 141     K-32  ENST00000514057.1
## 142     4894  ENST00000361681.2
## 143     4302  ENST00000457540.1
## 144      935  ENST00000361624.2
## 145     1393  ENST00000361624.2
## 146     4606  ENST00000361453.3
## 147     3375  ENST00000361681.2
## 148     K-32  ENST00000361851.1
## 149      727  ENST00000386347.1
## 150     1716  ENST00000361390.2
## 151  UID-142  ENST00000387347.2
## 152     3184  ENST00000361681.2
## 153     6219  ENST00000361453.3
## 154      727  ENST00000617998.4
## 155     4851  ENST00000362079.2
## 156     K-32  ENST00000577894.1
## 157     5109 ENST00000331825.10
## 158     4666  ENST00000457540.1
## 159     1349  ENST00000631211.1
## 160     6219  ENST00000361381.2
## 161     4118  ENST00000361789.2
## 162     2758  ENST00000386347.1
## 163      727  ENST00000336440.3
## 164     4118  ENST00000361624.2
## 165     1798  ENST00000627981.1
## 166     4851  ENST00000361227.2
## 167     5110 ENST00000331825.10
## 168     1716  ENST00000361681.2
## 169     4118  ENST00000389680.2
## 170     3723  ENST00000426721.2
## 171     2758  ENST00000627981.1
## 172     K-32  ENST00000581884.1
## 173     1079  ENST00000389680.2
## 174     2593  ENST00000534336.1
## 175     4606  ENST00000361681.2
## 176     1716  ENST00000361381.2
## 177     3723  ENST00000314401.3
## 178     2593  ENST00000619449.2
## 179     3864  ENST00000361453.3
## 180     3375  ENST00000361739.1
## 181     6219  ENST00000361335.1
## 182     4894  ENST00000361739.1
## 183     1393  ENST00000361899.2
## 184     6219  ENST00000361567.2
## 185    W-117  ENST00000222553.7
## 186      727  ENST00000421673.6
## 187     1079  ENST00000361381.2
## 188     1806  ENST00000619449.2
## 189     4894  ENST00000361851.1
## 190     2758  ENST00000560711.1
## 191     2758  ENST00000500989.2
## 192     3184  ENST00000361739.1
## 193     6219  ENST00000361390.2
## 194     1393  ENST00000361681.2
## 195      935  ENST00000361899.2
## 196     4606  ENST00000361789.2
## 197     4666  ENST00000386347.1
## 198     4606  ENST00000361335.1
## 199     3184  ENST00000361851.1
## 200     5047 ENST00000331825.10
## 201     1079  ENST00000361453.3
## 202     3864  ENST00000361335.1
## 203      727  ENST00000617585.1
## 204     4666  ENST00000560711.1
## 205     4894  ENST00000514057.1
## 206     1716  ENST00000361899.2
## 207     3184  ENST00000514057.1
## 208      727  ENST00000314888.9
## 209     2758  ENST00000577894.1
## 210     2758  ENST00000555997.1
## 211     5109 ENST00000309268.10
## 212     3723  ENST00000550536.5
## 213    W-117  ENST00000457540.1
## 214     4666  ENST00000577894.1
## 215     3723  ENST00000361264.8
## 216     3864  ENST00000361567.2
## 217     3864  ENST00000361390.2
## 218     6219  ENST00000361789.2
## 219     3375  ENST00000514057.1
## 220     K-32  ENST00000518964.5
## 221     4851  ENST00000457540.1
## 222     K-32  ENST00000517869.1
## 223   UID-51  ENST00000361381.2
## 224     5110 ENST00000309268.10
## 225     K-32  ENST00000500989.2
## 226     4894  ENST00000362079.2
## 227     3184  ENST00000362079.2
## 228     4666  ENST00000500989.2
## 229     2758  ENST00000617998.4
## 230     1716  ENST00000361453.3
## 231     5109  ENST00000335295.4
## 232     3375  ENST00000361851.1
## 233     2758  ENST00000517869.1
## 234     4118  ENST00000361899.2
## 235     2758  ENST00000518964.5
## 236     K-32  ENST00000361227.2
## 237     5047 ENST00000309268.10
## 238     6219  ENST00000361624.2
## 239      727  ENST00000375050.5
## 240     1079  ENST00000361567.2
## 241     3723  ENST00000535572.5
## 242     2758  ENST00000581884.1
## 243     2758  ENST00000336440.3
## 244     1079  ENST00000361390.2
## 245     4666  ENST00000581884.1
## 246     1079  ENST00000361789.2
## 247      727  ENST00000481999.1
## 248      727  ENST00000650186.1
## 249     3723  ENST00000413567.1
## 250     5047  ENST00000335295.4
## 251     3314  ENST00000222553.7
## 252     3723  ENST00000369512.2
## 253     4606  ENST00000361624.2
## 254     3723  ENST00000628092.2
## 255     1393  ENST00000361739.1
## 256      935  ENST00000361681.2
## 257     4894  ENST00000361227.2
## 258   UID-51  ENST00000389680.2
## 259     3723  ENST00000355085.3
## 260     2593  ENST00000379056.5
## 261     3184  ENST00000361227.2
## 262     3723  ENST00000587986.5
## 263     4666  ENST00000517869.1
## 264     4666  ENST00000518964.5
## 265   UID-51  ENST00000361335.1
## 266     2758  ENST00000429829.6
## 267     K-32  ENST00000457540.1
## 268     2758 ENST00000312635.10
## 269     1716  ENST00000361739.1
## 270     5109  ENST00000261267.6
## 271     2593  ENST00000309246.9
## 272     2593 ENST00000331825.10
## 273     4118  ENST00000361681.2
## 274     K-32  ENST00000617998.4
## 275   UID-51  ENST00000361567.2
## 276     3723  ENST00000565223.1
## 277     3723  ENST00000564973.1
## 278      727  ENST00000219281.7
## 279     3723  ENST00000480738.1
## 280     4666  ENST00000555997.1
## 281     1393  ENST00000361851.1
## 282     3723  ENST00000462363.6
## 283      727  ENST00000561743.5
## 284     5109  ENST00000391857.8
## 285     4851  ENST00000386347.1
## 286     3456  ENST00000457540.1
## 287     1079  ENST00000361335.1
## 288     2758  ENST00000271638.2
## 289     3723 ENST00000328024.10
## 290     3723  ENST00000393359.6
## 291     2758  ENST00000478109.1
## 292     2758  ENST00000378565.9
## 293      727  ENST00000524611.2
## 294     5109  ENST00000476268.6
## 295   UID-51  ENST00000361453.3
## 296     3375  ENST00000362079.2
## 297     4666  ENST00000378565.9
## 298      727  ENST00000645331.1
## 299     1716  ENST00000361851.1
## 300     3723  ENST00000373800.7
## 301     2593 ENST00000309268.10
## 302     3723  ENST00000355703.3
## 303     K-32  ENST00000555997.1
## 304      935  ENST00000362079.2
## 305     3723  ENST00000333511.8
## 306     3723  ENST00000509668.1
## 307     2758  ENST00000483366.5
## 308     3723  ENST00000530174.1
## 309     2758  ENST00000266682.9
## 310     4666  ENST00000617998.4
## 311     3723  ENST00000369448.3
## 312      935  ENST00000361739.1
## 313     3723  ENST00000428080.1
## 314     5109  ENST00000549690.1
## 315     2758  ENST00000375980.8
## 316     3723  ENST00000611658.1
## 317     4666  ENST00000336440.3
## 318     2758  ENST00000325602.5
## 319      727  ENST00000625598.1
## 320     1393  ENST00000514057.1
## 321     K-32 ENST00000312635.10
## 322     K-32  ENST00000558717.1
## 323     5110  ENST00000391857.8
## 324   UID-51  ENST00000361624.2
## 325     3723  ENST00000377095.9
## 326     1079  ENST00000361624.2
## 327     4851  ENST00000500989.2
## 328     K-32  ENST00000271638.2
## 329     3723  ENST00000342579.8
## 330     5109  ENST00000336906.5
## 331     4302  ENST00000592347.5
## 332     6219  ENST00000361899.2
## 333     3723  ENST00000642882.1
## 334     3723  ENST00000416426.6
## 335     K-32  ENST00000294507.3
## 336     4851  ENST00000577894.1
## 337     3723  ENST00000442934.6
## 338     5110  ENST00000476268.6
## 339     K-32  ENST00000478109.1
## 340     3723  ENST00000373610.7
## 341     3723  ENST00000373609.1
## 342      727  ENST00000597346.1
## 343     3375  ENST00000361227.2
## 344     4851  ENST00000560711.1
## 345     2758  ENST00000617585.1
## 346     5109  ENST00000642908.1
## 347     K-32  ENST00000263253.8
## 348     3723  ENST00000618006.4
## 349      727  ENST00000569588.1
## 350     3723  ENST00000366481.3
## 351     3723  ENST00000590751.5
## 352     3723  ENST00000593597.1
## 353     3723  ENST00000484971.1
## 354     3723  ENST00000588767.5
## 355     4666  ENST00000375980.8
## 356      727  ENST00000387439.1
## 357     3723  ENST00000219150.9
## 358     4666  ENST00000429829.6
## 359     3723  ENST00000493295.5
## 360     3723  ENST00000567099.1
## 361     2758  ENST00000387421.1
## 362      727  ENST00000270792.9
## 363     1079  ENST00000361899.2
## 364     K-32  ENST00000336440.3
## 365      935  ENST00000514057.1
## 366      727  ENST00000319041.6
## 367     3723  ENST00000256433.5
## 368     3723  ENST00000567034.5
## 369     3723  ENST00000419850.1
## 370     5110  ENST00000549690.1
## 371     3723  ENST00000587084.5
## 372     3723  ENST00000446198.5
## 373     5047  ENST00000261267.6
## 374   UID-51  ENST00000361390.2
## 375    W-117  ENST00000357727.6
## 376     5109  ENST00000615060.4
## 377     3723  ENST00000550454.5
## 378     3723  ENST00000480969.1
## 379     3723  ENST00000582401.5
## 380     2201  ENST00000314401.3
## 381     4118  ENST00000361739.1
## 382     3723 ENST00000293373.10
## 383     3723  ENST00000582406.1
## 384     2758  ENST00000421673.6
## 385     1393  ENST00000362079.2
## 386     5047  ENST00000391857.8
## 387     3723  ENST00000643836.1
## 388     4641  ENST00000650535.1
## 389     3723  ENST00000303115.7
## 390     4606  ENST00000362079.2
## 391     3723  ENST00000441514.1
## 392     3184  ENST00000457540.1
## 393      727  ENST00000485280.1
## 394     3723  ENST00000446947.6
## 395     3723  ENST00000353782.9
## 396     3723  ENST00000410031.5
## 397     K-32  ENST00000381605.8
## 398     3723  ENST00000585599.2
## 399     4894  ENST00000457540.1
## 400     5047  ENST00000615060.4
## 401     3723  ENST00000613419.4
## 402     3723  ENST00000519673.1
## 403     3723  ENST00000529681.5
## 404     3723  ENST00000359467.7
## 405     2758  ENST00000552192.5
## 406     K-32  ENST00000381603.7
## 407     4118  ENST00000361851.1
## 408     3723  ENST00000598759.1
## 409     3723  ENST00000477540.1
## 410     5047  ENST00000476268.6
## 411      727  ENST00000409016.8
## 412      727  ENST00000543406.1
## 413     3723  ENST00000193391.7
## 414     5110  ENST00000261267.6
## 415     1716  ENST00000361789.2
## 416     5110  ENST00000336906.5
## 417     3723  ENST00000510053.2
## 418     1079  ENST00000361739.1
## 419     3723  ENST00000647604.1
## 420     5110  ENST00000642908.1
## 421     2758  ENST00000558717.1
## 422      727  ENST00000461958.2
## 423     3723  ENST00000495101.5
## 424      935  ENST00000361851.1
## 425     4851  ENST00000555997.1
## 426      727  ENST00000306156.7
## 427     2758  ENST00000361050.3
## 428     2758  ENST00000645331.1
## 429     2758  ENST00000650627.1
## 430     2758  ENST00000524611.2
## 431     4666  ENST00000558717.1
## 432     2758  ENST00000559334.2
## 433     3723  ENST00000455245.1
## 434     6219  ENST00000361681.2
## 435     3723  ENST00000340967.2
## 436     3723  ENST00000342907.2
## 437     3723  ENST00000596209.3
## 438     3723  ENST00000393640.8
## 439     2758  ENST00000375050.5
## 440     3723  ENST00000529547.1
## 441     4851  ENST00000581884.1
## 442      727  ENST00000280800.4
## 443     3723  ENST00000432372.6
## 444     4641  ENST00000483366.5
## 445      727  ENST00000426500.5
## 446     3723  ENST00000521010.1
## 447     3723  ENST00000511359.1
## 448   UID-51  ENST00000361789.2
## 449     3723  ENST00000360270.6
## 450     5109  ENST00000222553.7
## 451     5109  ENST00000466254.1
## 452     4302  ENST00000367701.9
## 453      727  ENST00000487162.1
## 454     1716  ENST00000362079.2
## 455     3723  ENST00000453770.1
## 456      727  ENST00000623949.1
## 457     2758  ENST00000650535.1
## 458      727  ENST00000498388.1
## 459     3723  ENST00000374875.5
## 460     3723  ENST00000246024.6
## 461     4851  ENST00000517869.1
## 462     4118  ENST00000514057.1
## 463     K-32  ENST00000524611.2
## 464     5047  ENST00000549690.1
## 465     2758  ENST00000650186.1
## 466     4851  ENST00000617998.4
## 467     4666  ENST00000361050.3
## 468     K-32  ENST00000386347.1
## 469     K-32  ENST00000645331.1
## 470     4851  ENST00000518964.5
## 471     5109  ENST00000548900.1
## 472     4666  ENST00000645331.1
## 473     2758  ENST00000481999.1
## 474     3723  ENST00000262138.3
## 475     3723  ENST00000606389.5
## 476     2758  ENST00000263253.8
## 477     4666 ENST00000312635.10
## 478     3723 ENST00000356338.10
## 479     4666  ENST00000524611.2
## 480     3723 ENST00000358212.10
## 481     3723  ENST00000521699.5
## 482     3723  ENST00000367175.1
## 483     4302  ENST00000503611.5
## 484     5109  ENST00000530398.1
## 485     3723  ENST00000380361.7
## 486     3723  ENST00000591401.5
## 487     5109  ENST00000525722.1
## 488     3723  ENST00000584205.5
## 489      727  ENST00000425280.1
## 490     1393  ENST00000361227.2
## 491      727  ENST00000361198.9
## 492     4302  ENST00000306773.4
## 493     2593  ENST00000391857.8
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## 997     4302  ENST00000465564.1
## 998     4666  ENST00000398868.7
## 999   UID-51  ENST00000361681.2
## 1000    2201  ENST00000369151.7
# Transcripts<- fread("/Users/skogut/Desktop/Thesis/Transcripts_normalized_counts_WF.csv")
# ERV<- fread("/Users/skogut/Desktop/Thesis/ERV_normalized_counts_WF.csv")
Transcripts<- readRDS("Transcripts.RDS")
ERV<- readRDS("ERV.RDS")
# saveRDS(Transcripts, "Transcripts.RDS")
# saveRDS(ERV, "ERV.RDS")

dir.create("PositiveERV_Trans/")
## Warning in dir.create("PositiveERV_Trans/"): 'PositiveERV_Trans' already exists
# Create files ----------------------------------
# two sets of counts per file: 1 set from ERV, transcript per top 1000 pairs

########################################################
# FUNCTION file_builder
# description: creates a sest of random files for regression
# inputs: file_n = number f files to create
#         file_folder = name of folder for random file
#         file_size = c(min,max) number of rows in file
#        file_NA= average number of NA values per column
# outputs: creates a set of random files
# -----------------------------------------------------
file_builder <- function(file_n=1000,
                         file_folder= "PositiveERV_Trans/",
                         ERVdata= 1:1000,
                         Transcriptdata= 1:1000,
                         SelectPairs= 1:1000) {

for (i in 1:nrow(SelectPairs)) {
  
  var_x<- SelectPairs[i,1] # ERV
  var_y<-SelectPairs[i,2] # Transcript
 
  

   
  df<- data.frame(var_x = ERVdata[[ which(colnames(ERVdata)== var_x)]], var_y= Transcriptdata[[which(colnames(Transcriptdata)== var_y)]]) # bind into a data frame
  
  colnames(df)<- c(var_x, var_y)
  print(df)
  
  # create label for file name with padded zeroes
  file_label<- paste(file_folder, "PairFile",
                    formatC(i, 
                          width=3,
                             format= "d",
                             flag= "0"),
                             ".csv",
                         sep="")
  
  # set up data file and incorporate time stamp and minimal meta data
  write.table(cat("# Simulated random data filefor batch processing", "\n",
                  "# timestamp: ", as.character(Sys.time()), 
                  "\n",
                   "# SEK", "\n",
                 "#----------------------------", "\n",
                   "\n",
                   file=file_label,
                   row.names= "",
                   col.names= "",
                   sep= "") )
  
  # now add the data frame
  write.table(x=df,
              file= file_label,
              sep=",",
              row.names= FALSE,
              append=TRUE)
  
}

}  # end of file_builder
########################################################

# Create regression function/ graphing function ----------------------------------
########################################################
# FUNCTION reg_stats
# description: fits liner model extract m stats
# inputs: 2column data frame (x and y)
# outputs: slope, p-value, and r2
# -----------------------------------------------------
reg_stats <- function(d= NULL) {
    if( is.null(d)){
      x_var<- runif(10)
      y_var<- runif(10)
      d<- data.frame(x_var, y_var) }
  
  .<- lm(data=d, d[,2]~d[,1])
  .<- summary(.)
  stats_list<- list(Slope=.$coefficients[2,1],
                    pval= .$coefficients[2,4],
                    r2=.$r.squared)


return(stats_list)

}  # end of reg_stats
########################################################
# test


#######################################################
#global
file_folder<- "PositiveERV_Trans/"
n_files<- 100
file_out<- "StatsSummaryHW.csv"
file_names<- list.files(path= file_folder)
#######################################################
# running file builder to build files
file_builder(ERVdata = ERV, Transcriptdata = Transcripts, SelectPairs = SelectPairs)
# batch process by looping through individual files ----------------------------------

# create data frame to hold summary stats
ID<- seq_along(file_names)
file_name<- file_names
slope<- rep(NA, length(file_names))
pval<- rep(NA, length(file_names))
r2<- rep(NA, length(file_names))

stats_out<- data.frame(ID, file_name, slope, pval, r2)


# batch process by looping through individual files
for(i in seq_along(file_names)) {
  
  data<- read.table(file=paste(file_folder, file_names[i],
                               sep=""),
                    sep=",", 
                    header= TRUE)
  
  .<- reg_stats(d=data) # pull out regression stats from clean file
  stats_out[i,3:5]<- unlist(.) # unlist, copy into last three  cols
}

# set up an output file and incorporate time stamp and minimal metadata

write.table(cat( "# Summary stats for",
                 "batch processing of regression models",
                 "\n",
                 "# timestamp: ", as.character(Sys.time()),
                 "\n",
                 file= file_out,
                 row.names= "",
                 col.names="",
                 sep= ""))
## ""
# set up an output file and incorporate time stamp and minimal metadata
# now add the data frame
write.table(x=stats_out,
           file=file_out,
           row.names=FALSE,
           col.names=TRUE,
           sep= ",",
           append=TRUE)
## Warning in write.table(x = stats_out, file = file_out, row.names = FALSE, :
## appending column names to file
file_out<- "StatsSummaryHW.csv"

# arranging data to find something meaningful

stats_out<- arrange(stats_out, desc(r2))
head(stats_out)
##    ID       file_name     slope         pval        r2
## 1 950 PairFile949.csv  842.8526 2.313595e-52 0.9844926
## 2 824 PairFile823.csv  897.8977 1.133303e-27 0.8821019
## 3 579 PairFile578.csv 1266.0763 1.569202e-27 0.8807268
## 4 976 PairFile975.csv  789.6071 2.540270e-27 0.8786620
## 5 796 PairFile795.csv  924.5246 5.063990e-27 0.8756426
## 6 999 PairFile998.csv  777.0859 9.411610e-27 0.8728661
# plotting quick scatterplots to look for outliers, in the top 50 pairs when ordered by r2

for (i in 1:50) {
data<- read.table(file=paste(file_folder, stats_out$file_name[i],
                               sep=""),
                    sep=",", 
                    header= TRUE)
p<- qplot(x=data[,1],
      y=data[,2],
      geom= c("smooth", "point"), method= "lm", 
xlim= c(0, 25),
ylim= c(0,10000))
 print(i)
print(p)

 
 Sys.sleep(1.5)
}
## Warning: Ignoring unknown parameters: method
## [1] 1
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 2
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 3
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 4
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 5
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 6
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 7
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 8
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 9
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 10
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 11
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 44 rows containing non-finite values (stat_smooth).
## Warning: Removed 44 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 12
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 13
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 14
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 18 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 15
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 16
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 37 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 17
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 19 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 18
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 40 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 19
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 20
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 28 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 21
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 2 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 22
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 23
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 24
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 39 rows containing non-finite values (stat_smooth).
## Warning: Removed 2 rows containing missing values (geom_smooth).
## Warning: Removed 39 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 25
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 10 rows containing non-finite values (stat_smooth).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 26
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 41 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 27
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 33 rows containing missing values (geom_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 28
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 35 rows containing non-finite values (stat_smooth).
## Warning: Removed 35 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 29
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 15 rows containing non-finite values (stat_smooth).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 30
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 3 rows containing non-finite values (stat_smooth).
## Warning: Removed 3 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 31
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning -
## Inf
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 32
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 33
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 22 rows containing non-finite values (stat_smooth).
## Warning: Removed 22 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 34
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 35
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 11 rows containing non-finite values (stat_smooth).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 36
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 53 rows containing non-finite values (stat_smooth).
## Warning: Removed 53 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 37
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 38
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 39
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 10 rows containing non-finite values (stat_smooth).
## Warning: Removed 10 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 40
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 45 rows containing non-finite values (stat_smooth).
## Warning: Removed 45 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 41
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 44 rows containing non-finite values (stat_smooth).
## Warning: Removed 44 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 42
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 43
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 7 rows containing non-finite values (stat_smooth).
## Warning: Removed 7 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 44
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 7 rows containing non-finite values (stat_smooth).
## Warning: Removed 7 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 45
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 46
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 47
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 34 rows containing non-finite values (stat_smooth).
## Warning: Removed 34 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 48
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 11 rows containing non-finite values (stat_smooth).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 49
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 52 rows containing non-finite values (stat_smooth).
## Warning: Removed 52 rows containing missing values (geom_point).
## Warning: Ignoring unknown parameters: method

## [1] 50
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 58 rows containing non-finite values (stat_smooth).
## Warning: Removed 58 rows containing missing values (geom_point).